ISMsi2
- Family IS3
- Group IS407
Isoform Synonym(s)
| Accession number | Transposition | Origin | Host |
|---|---|---|---|
| NC_011666 | ND | Methylocella silvestris | Methylocella silvestris BL2 |
DNA section
IS Length : 1332 bp
Ends
IR Length : 18/26
IRL : TGGTCTGCGCCCCTTGAAGTGATCCATGCCGTATGTTGGTCCGCGGACCC
IRR : TGGCCTGTCCCCGAGGTGTGATCCAGTTTCAATGTTAGTGCATGGCAGGC
Insertion site
| Left flank | Direct repeat | Right flank | DR Length |
|---|---|---|---|
| TGATCGGGGT | GG | CCCATTAGCG | 2 |
DNA sequence
TGGTCTGCGCCCCTTGAAGTGATCCATGCCGTATGTTGGTCCGCGGACCCTTTGGAAGGATGGAGCGATGGGAATAAAGGGGCACAAACCGGAGGAGATC
GTCGCCAAGCTGCGTCAGGTTGATATTCTGACGGCGCAAGGCAAGTCGATTGCCGATGCGGTGAAAACGATCGCTGTGACGGAGGCGACGTACTTCCGCT
GGCGCGCGGAGTATGGCGGCCTGAAGAGCGGCCAGGTCAAGCGGCTGAAGGATCTGGAGCTGGAGAACGCCCGGCTGCGGCGGGCGGCGTCGGACCTGAC
CCTGGACAAGCTGATTTGACCGAAGCCACGCGGGGACACTTCTAAGCCCCGCCCGTCGCCGCGCCTGCGTGGACAAGGTCAAAGCCGAGCTGAGAGTGTC
GGAGCGTCGCGCCTGCGCGGCGCTCCGGCAGCCCCGCTCCACACAGCGCAAGCCAGCCCGCGGCCGCGATGACGAGGCGGCTCTGACCGCCGACATCGTC
GAGCTGGCCAAGGCTTATGGCCGCTACGGCTATCGGCGGATCACGGCTTTGCTGCGCCATGCTGGCTGGGTCGTGAACGCCAAGCGGGTGCAGCGGATCT
GGCGCGCAGACAAGTTCACGCAGTCTGCGCAACAGCGCGACTGCGAGGGGCTGAAAGTCCCACAGAAACACCCAAAACGCGGCAGGCTCTGGCTGAACGA
CGGCTCTTGCGTGCGCCCGCGCGCCGAGCGGCCCAACCATGTCTGGTCCTATGACTTCGTCGCGGATCGGACCCAAGATGGACGGAAGTTCCGTATGCTC
TGTTTGATCGACGAGTTCACCCGCGAGGCCCTGGCCATCCAGGTCAAACGCCGGCTCAACGCCACCGACGTGCTGGAGACCTTGGCCGATCTGATGATCC
TGCGCGGAACGCCAGCCTATGTTCGGTCGGACAATGGCCCGGAGTTCATCGCCGTGGCCCTGCGCGAATGGATCGCCGCCGTCGGTTCAAAGACGGCCTA
TATCGAGCCCGGCAGCCCGTGGGAGAATGGCGCCTGCGAGAGCTTCAATTCGAATCTCCGCGACGAGCTGCTCAATGGTGAGCTGTTCTTCAGCCCAGCC
GAGGCTCAGGCGATGATCGAGGCCTGGCGGCGGCATTTCAACGCCGTGCGCCCACACAGCTCGCTCGGTTACCGATCGCCAGCGCCCGAGACAATTATTC
CCTGCGGCGGAAACATCGCGCCATGGGCGAGCGCGCCAGCTGTGGGAGCCGCGCGCCCGCCCACACCAACCATGGCGTCAGAGCCTGCCATGCACTAACA
TTGAAACTGGATCACACCTCGGGGACAGGCCA
GTCGCCAAGCTGCGTCAGGTTGATATTCTGACGGCGCAAGGCAAGTCGATTGCCGATGCGGTGAAAACGATCGCTGTGACGGAGGCGACGTACTTCCGCT
GGCGCGCGGAGTATGGCGGCCTGAAGAGCGGCCAGGTCAAGCGGCTGAAGGATCTGGAGCTGGAGAACGCCCGGCTGCGGCGGGCGGCGTCGGACCTGAC
CCTGGACAAGCTGATTTGACCGAAGCCACGCGGGGACACTTCTAAGCCCCGCCCGTCGCCGCGCCTGCGTGGACAAGGTCAAAGCCGAGCTGAGAGTGTC
GGAGCGTCGCGCCTGCGCGGCGCTCCGGCAGCCCCGCTCCACACAGCGCAAGCCAGCCCGCGGCCGCGATGACGAGGCGGCTCTGACCGCCGACATCGTC
GAGCTGGCCAAGGCTTATGGCCGCTACGGCTATCGGCGGATCACGGCTTTGCTGCGCCATGCTGGCTGGGTCGTGAACGCCAAGCGGGTGCAGCGGATCT
GGCGCGCAGACAAGTTCACGCAGTCTGCGCAACAGCGCGACTGCGAGGGGCTGAAAGTCCCACAGAAACACCCAAAACGCGGCAGGCTCTGGCTGAACGA
CGGCTCTTGCGTGCGCCCGCGCGCCGAGCGGCCCAACCATGTCTGGTCCTATGACTTCGTCGCGGATCGGACCCAAGATGGACGGAAGTTCCGTATGCTC
TGTTTGATCGACGAGTTCACCCGCGAGGCCCTGGCCATCCAGGTCAAACGCCGGCTCAACGCCACCGACGTGCTGGAGACCTTGGCCGATCTGATGATCC
TGCGCGGAACGCCAGCCTATGTTCGGTCGGACAATGGCCCGGAGTTCATCGCCGTGGCCCTGCGCGAATGGATCGCCGCCGTCGGTTCAAAGACGGCCTA
TATCGAGCCCGGCAGCCCGTGGGAGAATGGCGCCTGCGAGAGCTTCAATTCGAATCTCCGCGACGAGCTGCTCAATGGTGAGCTGTTCTTCAGCCCAGCC
GAGGCTCAGGCGATGATCGAGGCCTGGCGGCGGCATTTCAACGCCGTGCGCCCACACAGCTCGCTCGGTTACCGATCGCCAGCGCCCGAGACAATTATTC
CCTGCGGCGGAAACATCGCGCCATGGGCGAGCGCGCCAGCTGTGGGAGCCGCGCGCCCGCCCACACCAACCATGGCGTCAGAGCCTGCCATGCACTAACA
TTGAAACTGGATCACACCTCGGGGACAGGCCA
Recoding section
- Recoding by frameshift
- Frame
- Type
- Experimentally demonstrated
Stimulators :
- Shine-Dalgarno sequence :
- Secondary structure :
Recoding motif :
Protein section
ORF number : 3
ORF 1
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 252 bp | 83 aa | 68 | 319 | + | No |
Description : First part of the transposase
ORF sequence :
MGIKGHKPEEIVAKLRQVDILTAQGKSIADAVKTIAVTEATYFRWRAEYGGLKSGQVKRLKDLELENARLRRAASDLTLDKLI
Blast result :ORF 2
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 984 bp | 327 aa | 315 | 1298 | + | No |
Description : Second part of the transposase
ORF sequence :
FDRSHAGTLLSPARRRACMDKVKAELRVSERRACAALRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADK
FTQSAQQRDCEGLKVPQKHPKRGRLWLNDGSCVRPRAERPNHVWSYDFVADRTQDGRKFRMLCLIDEFTREALAIQVKRRLNATDVLETLADLMILRGTP
AYVRSDNGPEFIAVALREWIAAVGSKTAYIEPGSPWENGACESFNSNLRDELLNGELFFSPAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGN
IAPWASAPAVGAARPPTPTMASEPAMH
FTQSAQQRDCEGLKVPQKHPKRGRLWLNDGSCVRPRAERPNHVWSYDFVADRTQDGRKFRMLCLIDEFTREALAIQVKRRLNATDVLETLADLMILRGTP
AYVRSDNGPEFIAVALREWIAAVGSKTAYIEPGSPWENGACESFNSNLRDELLNGELFFSPAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGN
IAPWASAPAVGAARPPTPTMASEPAMH
Blast result :ORF 3
| Length | Begin | End | Strand | Fusion ORF | |
|---|---|---|---|---|---|
| 1231 bp | 410 aa | 68 | 1298 | + | Yes |
Chemistry : DDE
ORF sequence :
MGIKGHKPEEIVAKLRQVDILTAQGKSIADAVKTIAVTEATYFRWRAEYGGLKSGQVKRLKDLELENARLRRAASDLTLDKLIFDRSHAGTLLSPARRRA
CMDKVKAELRVSERRACAALRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADKFTQSAQQRDCEGLKVPQ
KHPKRGRLWLNDGSCVRPRAERPNHVWSYDFVADRTQDGRKFRMLCLIDEFTREALAIQVKRRLNATDVLETLADLMILRGTPAYVRSDNGPEFIAVALR
EWIAAVGSKTAYIEPGSPWENGACESFNSNLRDELLNGELFFSPAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGNIAPWASAPAVGAARPPT
PTMASEPAMH
CMDKVKAELRVSERRACAALRQPRSTQRKPARGRDDEAALTADIVELAKAYGRYGYRRITALLRHAGWVVNAKRVQRIWRADKFTQSAQQRDCEGLKVPQ
KHPKRGRLWLNDGSCVRPRAERPNHVWSYDFVADRTQDGRKFRMLCLIDEFTREALAIQVKRRLNATDVLETLADLMILRGTPAYVRSDNGPEFIAVALR
EWIAAVGSKTAYIEPGSPWENGACESFNSNLRDELLNGELFFSPAEAQAMIEAWRRHFNAVRPHSSLGYRSPAPETIIPCGGNIAPWASAPAVGAARPPT
PTMASEPAMH
Blast result :
Comments
ISMsi2 is 75 % aa similar to ISMex5. The third ORF is a putative ORFAB transposase reconstructed in silico by possible -1 frameshift.
References
1] ISfinder annotation (2009)
2] Lucas,S., Lucas,S., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Forester,B., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinnikova,G., Dunfield,P.F., Dedysh,S.N., Liesack,W., Stott,M.B., Smirnova,A.V., Alam,M., Chen,Y., Murrell,J.C. and Richardson,P.(2008) Direct submission GenBank.
2] Lucas,S., Lucas,S., Lapidus,A., Glavina del Rio,T., Dalin,E., Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Forester,B., Larimer,F., Land,M., Hauser,L., Kyrpides,N., Ovchinnikova,G., Dunfield,P.F., Dedysh,S.N., Liesack,W., Stott,M.B., Smirnova,A.V., Alam,M., Chen,Y., Murrell,J.C. and Richardson,P.(2008) Direct submission GenBank.